UpSet Plot

UpSet plot for Domain Architectures vs Domains and Genomic Contexts vs Domain Architectures.

Usage

upset.plot(
  query_data = "toast_rack.sub",
  colname = "DomArch",
  cutoff = 90,
  RowsCutoff = FALSE,
  text.scale = 1.5,
  point.size = 2.2,
  line.size = 0.8
)

Arguments

query_data

Data frame of protein homologs with the usual 11 columns + additional word columns (0/1 format). Default is toast_rack.sub

cutoff

Numeric. Cutoff for word frequency. Default is 90.

text.scale

Allows scaling of axis title, tick lables, and numbers above the intersection size bars. text.scale can either take a universal scale in the form of an integer, or a vector of specific scales in the format: c(intersection size title, intersection size tick labels, set size title, set size tick labels, set names, numbers above bars)

line.size

Details

For "da2doms" you would need the file DA.doms.wc as well as the column query_data$DomArch.norep

For "gc2da", you would need the file GC.DA.wc as well as the column query_data$GenContext.norep

Note

Please refer to the source code if you have alternate file formats and/or column names.

Author

Janani Ravi

Examples

if (FALSE) { # \dontrun{
upset.plot(pspa.sub, 10, "da2doms")
} # }